Zebrafish vs C.savignyi Translated Blat alignments

Zebrafish (Danio rerio, Zv9) and C.savignyi (Ciona savignyi, CSAV2.0) were aligned using the Translated Blat alignment algorithm (Kent W, Genome Res., 2002;12(4):656-64)
in Ensembl release 60. Zebrafish was used as the reference species. After running Translated Blat, the raw Translated Blat alignment blocks
are chained according to their location in both genomes. During the final netting process, the best
sub-chain is chosen in each region on the reference species.

Configuration parameters

Parameter

Value

Minimum score (minScore)

30

Database type (t)

dnax

Query type (q)

dnax

Mask out repeats (mask)

lower

Mask out repeats on query (qMask)

lower

Chunking parameters

Zebrafish

C.savignyi

Chunk size

1,000,000

25,000

Overlap

10,000

10,000

Group set size

100,000,000

10,000,000

Masking options

{default_soft_masking => 1}

{default_soft_masking => 1}

Results

Number of alignment blocks: 65,261

Genome coverage (bp)

Coding exon coverage (bp)

Danio rerio

Uncovered: 1,406,166,733 out of 1,412,464,843Covered: 6,298,110 out of 1,412,464,843

Uncovered: 37,400,514 out of 42,417,757Matches: 3,446,895 out of 42,417,757Mismatches: 1,570,176 out of 42,417,757Insertions: 172 out of 42,417,757

Ciona savignyi

Uncovered: 173,890,161 out of 176,989,013Covered: 3,098,852 out of 176,989,013

Uncovered: 11,371,130 out of 13,806,906Matches: 1,661,516 out of 13,806,906Mismatches: 773,979 out of 13,806,906Insertions: 281 out of 13,806,906